Rise of The Dragon or Heart of China (both Dynamix games) I can't remember which, refuses to install in anything but pure DOS. I'll have to dig out my floppies to see. I believe that there may be issues with the original SQ1 on floppy, which I don't have, so I can't confirm it. I once linked to a thread on Ken Williams' site about the copy protection that Sierra used to use for their floppies.

Does Inner Space (http://www.sdispace.com/) count? When you buy it you get the game on a floppy disk and on installing it writes something onto the floppy that is tied to the boot sector of your hard drive. To install the game on another PC you have to uninstall it first from the first machine.
This scheme only works under Dosbox if you use and boot from a hdd image, under normal Dosbox whatever information it reads is not availlable or not fixed, whatever 😀

There is one known workaround: Apparently the company also once made CD-Roms with the game. With these the CD-Rom is the copy protection and images of this work fine in normal Dosbox 😀
(but these CD-Roms are not easy to get a hold of)